Alignments for a candidate for hisC in Sinorhizobium meliloti 1021

GapMind for Amino acid biosynthesis

Alignments for a candidate for hisC in Sinorhizobium meliloti 1021

Align histidinol-phosphate aminotransferase [EC:2.6.1.9] (characterized)
to candidate SMc00710 SMc00710 histidinol-phosphate aminotransferase

Query= reanno::Phaeo:GFF2492
         (361 letters)



>FitnessBrowser__Smeli:SMc00710
          Length = 368

 Score =  356 bits (913), Expect = e-103
 Identities = 186/358 (51%), Positives = 235/358 (65%), Gaps = 8/358 (2%)

Query: 5   APQPGILDIALYEGGAAHVKGMSNVTKLSSNENPLGPSPKAIEAMQAAVSEMHRYPSSDH 64
           AP+ GILDIA Y  G  H  G++ V KLSSNE PLG SP+AIEA Q A   + RYP    
Sbjct: 9   APRSGILDIAAYVPGKEHAPGVAKVHKLSSNETPLGASPRAIEAFQKAAFNLERYPDGQA 68

Query: 65  SGLRQAIGEVYGLPMEQIICGAGSDEIITFLCQAYAGPGDEVLFTEHGFAMYRISALAAG 124
           + L++AI  V+GL    I+CG GSDE++  LC  Y GPGDE + TEHGF +Y+I   A+G
Sbjct: 69  NALKEAIAAVHGLNPANILCGNGSDELLGLLCHTYLGPGDEGIVTEHGFLVYKIQITASG 128

Query: 125 ATPVEVAERDRVTDVDALLAGCTERTRLVFIANPNNPTGTMIGMADLARLADGLPKGALL 184
            TPV V ER    DVDA+LA  TERT++VFIANP NPTGT I + ++ RL  GLP G LL
Sbjct: 129 GTPVTVKERQERVDVDAILAAVTERTKIVFIANPANPTGTYIPVEEVRRLHAGLPAGVLL 188

Query: 185 VLDGAYAEYV--EGYDAGAALVANRDNVVMTRTFSKIYGLGGARVGWGYAPKPIIDVLNR 242
           VLD AYAEYV    Y+AG  LV++  NVVMTRTFSKIYGL G R+GW YAP+ +++ L+R
Sbjct: 189 VLDAAYAEYVRRNDYEAGLELVSSNRNVVMTRTFSKIYGLAGLRIGWMYAPRDVVEALDR 248

Query: 243 VRGPFNLSSTALAGAEAAVRDTDYTEHCRKENAKWRTWLAEALAELGVPSDTSCANFILA 302
           VRGPFNL++ A+A   AA+RD  +      +N  W   + +AL ++G+    S  NF+L 
Sbjct: 249 VRGPFNLNAAAIAAGAAAIRDQAFVAAAVDQNHTWLAKIGQALTDIGLRVTPSVTNFVLI 308

Query: 303 RFASPEEAGA----CDAFLQSRGLIVRRVTGYKLPAALRITVGDETACNALVAAMKVF 356
            F  PEEAG      DA+L SRG I+R V  Y  P ALR+T+G E A   +VAA+  F
Sbjct: 309 HF--PEEAGMSASDADAYLTSRGFILRAVGAYGFPNALRMTIGSEEANKGVVAALTEF 364


Lambda     K      H
   0.318    0.134    0.399 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 405
Number of extensions: 16
Number of successful extensions: 3
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 361
Length of database: 368
Length adjustment: 29
Effective length of query: 332
Effective length of database: 339
Effective search space:   112548
Effective search space used:   112548
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 49 (23.5 bits)

Align candidate SMc00710 SMc00710 (histidinol-phosphate aminotransferase)
to HMM TIGR01141 (hisC: histidinol-phosphate transaminase (EC 2.6.1.9))

# hmmsearch :: search profile(s) against a sequence database
# HMMER 3.3.1 (Jul 2020); http://hmmer.org/
# Copyright (C) 2020 Howard Hughes Medical Institute.
# Freely distributed under the BSD open source license.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query HMM file:                  ../tmp/path.aa/TIGR01141.hmm
# target sequence database:        /tmp/gapView.31082.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01141  [M=349]
Accession:   TIGR01141
Description: hisC: histidinol-phosphate transaminase
Scores for complete sequences (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Sequence                           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
    9.7e-91  290.2   0.0    1.1e-90  290.0   0.0    1.0  1  lcl|FitnessBrowser__Smeli:SMc00710  SMc00710 histidinol-phosphate am


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Smeli:SMc00710  SMc00710 histidinol-phosphate aminotransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  290.0   0.0   1.1e-90   1.1e-90       2     348 ..      12     363 ..      11     364 .. 0.96

  Alignments for each domain:
  == domain 1  score: 290.0 bits;  conditional E-value: 1.1e-90
                           TIGR01141   2 ekikklepYqpgarelgek.evvkLnsnEnPfgpsekvkealkeelkklhrYpdpqalelkealakylgveeeni 75 
                                           i ++++Y+pg+++ ++  +v kL+snE P+g s++++ea+++++ +l+rYpd qa +lkea+a++ g++++ni
  lcl|FitnessBrowser__Smeli:SMc00710  12 SGILDIAAYVPGKEHAPGVaKVHKLSSNETPLGASPRAIEAFQKAAFNLERYPDGQANALKEAIAAVHGLNPANI 86 
                                         678899******88777776899**********************99**************************** PP

                           TIGR01141  76 llgnGsdelielliraflepgdavlvleptysmYevsakiagaevkevplkedgqedleavleaakekvklvfla 150
                                         l gnGsdel+ ll++++l pgd+ +v+e+ + +Y++  ++ g   ++v+ +++ + d++a+l+a++e++k+vf+a
  lcl|FitnessBrowser__Smeli:SMc00710  87 LCGNGSDELLGLLCHTYLGPGDEGIVTEHGFLVYKIQITASGGTPVTVKERQE-RVDVDAILAAVTERTKIVFIA 160
                                         *************************************************9999.69******************* PP

                           TIGR01141 151 sPnnPtGnllkreeiekvleev.edalVVvDeAYieFsee...asvlellaeypnlvvlrTlSKafgLAglRvGy 221
                                         +P nPtG+++  ee++++ +   + +l V+D AY e+ ++   +  lel++   n+v++rT+SK++gLAglR+G 
  lcl|FitnessBrowser__Smeli:SMc00710 161 NPANPTGTYIPVEEVRRLHAGLpAGVLLVLDAAYAEYVRRndyEAGLELVSSNRNVVMTRTFSKIYGLAGLRIGW 235
                                         **********************88**************99888889***************************** PP

                           TIGR01141 222 aianaeiiealekvrapynvsslaleaavaalrdsdkiektveevkkererlleelkkleglevyeSkaNFvlik 296
                                         ++a  +++eal++vr p+n++  a +a+ aa+rd++++++ v+++    + + ++l+++ gl+v +S +NFvli+
  lcl|FitnessBrowser__Smeli:SMc00710 236 MYAPRDVVEALDRVRGPFNLNAAAIAAGAAAIRDQAFVAAAVDQNHTWLAKIGQALTDI-GLRVTPSVTNFVLIH 309
                                         ***********************************************************.8************** PP

                           TIGR01141 297 vke....daeelleallekgiivRdlksaeglleeclRitvGtreenerllealke 348
                                         ++e     a+++   l+ +g+i+R ++++ g+ +++lR+t+G++e n+ +++al e
  lcl|FitnessBrowser__Smeli:SMc00710 310 FPEeagmSASDADAYLTSRGFILRAVGAY-GF-PNALRMTIGSEEANKGVVAALTE 363
                                         **98888788888899***********99.86.********************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (349 nodes)
Target sequences:                          1  (368 residues searched)
Passed MSV filter:                         1  (1); expected 0.0 (0.02)
Passed bias filter:                        1  (1); expected 0.0 (0.02)
Passed Vit filter:                         1  (1); expected 0.0 (0.001)
Passed Fwd filter:                         1  (1); expected 0.0 (1e-05)
Initial search space (Z):                  1  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 9.31
//
[ok]

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

the paper from 2019 on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer
changes to Amino acid biosynthesis since the publication.

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory

GapMind for Amino acid biosynthesis